Gene expression and how we measure it
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You may recall from the molecular biology sections of this guide, that during gene expression, the information in a gene is transcribed, or copied, into a molecule called RNA. The RNA molecule is then translated into a specific protein or other functional molecule. Gene expression is regulated at various steps in this process, allowing cells to turn genes on or off as needed to produce the proteins and other molecules they require.
Gene expression is an important aspect of how an organism's traits are inherited and how they can evolve over time. It is also a key factor in how cells and tissues develop and function.
Start by reading a short introduction about the RNA-sequencing data analysis and gene expression.
There are several techniques that can be used to measure gene expression, including:
Northern blotting: This technique involves isolating RNA from cells or tissues and separating it based on size using electrophoresis. The separated RNA is then transferred to a membrane, and specific RNA molecules are detected using a labeled probe.
Reverse transcription polymerase chain reaction (RT-PCR): This technique involves using the enzyme reverse transcriptase to make a complementary DNA (cDNA) copy of RNA. The cDNA is then amplified using polymerase chain reaction (PCR), and the amount of amplified cDNA is measured.
Microarrays: A microarray is a glass slide or other substrate with thousands of tiny spots of DNA, each representing a different gene. RNA from cells or tissues is labeled with a fluorescent dye and added to the microarray. The amount of fluorescence at each spot is measured, and this can be used to determine the relative expression levels of different genes.
RNA sequencing: This technique involves sequentially reading the nucleotide bases in an RNA molecule, which allows for the precise measurement of the abundance of specific RNA molecules.
Protein expression: Gene expression can also be measured by analyzing the levels of the proteins encoded by specific genes. This can be done using techniques such as western blotting, immunoprecipitation, and mass spectrometry.
In this section, you will be introduced to NGS RNA sequencing data analysis for gene expression measurement. Visit this subchapters 8.3.1 to 8.3.3 to get a theoretical understanding of the pipeline. Optionally, you may try out the practical exercises with R as well. We will have a separate tutorial on how to perform normalization and differential expression analysis in the next sections.